University of Oklahoma

About: University of Oklahoma is a education organization based out in Norman, Oklahoma, United States. It is known for research contribution in the topics: Population & Radar. The organization has 25269 authors who have published 52609 publications receiving 1821706 citations. The organization is also known as: OU & Oklahoma University.

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

Abstract: The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

Empirical approach to estimating the composition of the continental crust

Abstract: The continental crust has ultimately been extracted from the mantle and knowledge of its composition is therefore fundamental to an understanding of the chemical evolution of the Earth. Attempts to model its average chemistry are complicated by marked vertical and lateral chemical and lithological heterogeneity1–3 and by problems of sampling the deeper levels of the crust. We have adopted a different, empirical, approach to try and take account of geophysical and isotopic constraints by considering the major and trace element chemistry of components which are typical of various crustal levels and ages. Our estimate differs from that of the ‘andesitic’ model in being more siliceous and having a more fractionated rare earth element pattern. Its higher Th, U and K contents generate a higher heat production of 0.95 µW m−3 compared with previous estimates of 0.75–0.91 µW m−3.

The global, ppGpp‐mediated stringent response to amino acid starvation in Escherichia coli

Abstract: The stringent response to amino acid starvation, whereby stable RNA synthesis is curtailed in favor of transcription of amino acid biosynthetic genes, is controlled by the alarmone ppGpp. To elucidate the extent of gene expression effected by ppGpp, we designed an experimental system based on starvation for isoleucine, which could be applied to both wildtype Escherichia coli and the multi-auxotrophic relA spoT mutant (ppGpp0). We used microarrays to profile the response to amino acid starvation in both strains. The wildtype response included induction of the general stress response, down regulation of genes involved in production of macromolecular structures, and comprehensive restructuring of metabolic gene expression, but not induction of amino acid biosynthesis genes en masse. This restructuring of metabolism was confirmed using kinetic Biolog assays. These responses were profoundly altered in the ppGpp0 strain. Furthermore, upon isoleucine starvation, the ppGpp0 strain exhibited a larger cell size and continued growth, ultimately producing 50% more biomass than the wildtype, despite producing a similar amount of protein. This mutant phenotype correlated with aberrant gene expression in diverse processes including DNA replication, cell division, and fatty acid and membrane biosynthesis. We present a model that expands and functionally integrates the ppGpp-mediated stringent response to include control of virtually all macromolecular synthesis and intermediary metabolism.

Improved luminosity determination in pp collisions at root s=7 TeV using the ATLAS detector at the LHC

Abstract: The luminosity calibration for the ATLAS detector at the LHC during pp collisions at root s = 7 TeV in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at root s = 7 TeV. A luminosity uncertainty of delta L/L = +/- 3.5 % is obtained for the 47 pb(-1) of data delivered to ATLAS in 2010, and an uncertainty of delta L/L = +/- 1.8 % is obtained for the 5.5 fb(-1) delivered in 2011.

Feature-based molecular networking in the GNPS analysis environment.

Abstract: Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.